---
OA_place: repository
OA_type: green
_id: '12737'
abstract:
- lang: eng
text: The substitution of heavier, more metallic atoms into classical organic ligand
frameworks provides an important strategy for tuning ligand properties, such as
ligand bite and donor character, and is the basis for the emerging area of main-group
supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3]
[E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their
coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3]
(E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination
modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints
at the bridgehead and with their more remote N-donor atoms. A particular feature
is the adaptive nature of these new ligands, with the ability to adjust coordination
mode in response to the hard–soft character of coordinated metal ions, influenced
also by the character of the bridgehead atom (Sb or Bi). These features can be
seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6)
(2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented
intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual
N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands
[E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their
complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family
with a range of metals. The greater polarity of the Bi–C bond in 2 results in
ligand transfer reactions with Au(I). Although this reactivity is not in itself
unusual, the characterization of several products by single-crystal X-ray diffraction
provides snapshots of the ligand transfer reaction involved, with one of the products
(the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core
in which the shortest Au → Bi donor–acceptor bond to date is observed.
acknowledgement: The authors thank the Walters-Kundert Studentship of Selwyn College
(scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146),
the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science
and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities
(MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER,
UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander
Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc.
(I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were
carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are
grateful for the calculation time used.
article_processing_charge: No
article_type: original
author:
- first_name: Álvaro
full_name: García-Romero, Álvaro
last_name: García-Romero
- first_name: Jessica E.
full_name: Waters, Jessica E.
last_name: Waters
- first_name: Rajesh B
full_name: Jethwa, Rajesh B
id: 4cc538d5-803f-11ed-ab7e-8139573aad8f
last_name: Jethwa
orcid: 0000-0002-0404-4356
- first_name: Andrew D.
full_name: Bond, Andrew D.
last_name: Bond
- first_name: Annie L.
full_name: Colebatch, Annie L.
last_name: Colebatch
- first_name: Raúl
full_name: García-Rodríguez, Raúl
last_name: García-Rodríguez
- first_name: Dominic S.
full_name: Wright, Dominic S.
last_name: Wright
citation:
ama: García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group
15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry.
2023;62(11):4625-4636. doi:10.1021/acs.inorgchem.3c00057
apa: García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A.
L., García-Rodríguez, R., & Wright, D. S. (2023). Highly adaptive nature of
group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry.
American Chemical Society. https://doi.org/10.1021/acs.inorgchem.3c00057
chicago: García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond,
Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive
Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic
Chemistry. American Chemical Society, 2023. https://doi.org/10.1021/acs.inorgchem.3c00057.
ieee: Á. García-Romero et al., “Highly adaptive nature of group 15 tris(quinolyl)
ligands─studies with coinage metals,” Inorganic Chemistry, vol. 62, no.
11. American Chemical Society, pp. 4625–4636, 2023.
ista: García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez
R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies
with coinage metals. Inorganic Chemistry. 62(11), 4625–4636.
mla: García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl)
Ligands─studies with Coinage Metals.” Inorganic Chemistry, vol. 62, no.
11, American Chemical Society, 2023, pp. 4625–36, doi:10.1021/acs.inorgchem.3c00057.
short: Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R.
García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636.
date_created: 2023-03-19T23:00:59Z
date_published: 2023-03-08T00:00:00Z
date_updated: 2025-04-24T11:32:09Z
day: '08'
department:
- _id: StFr
doi: 10.1021/acs.inorgchem.3c00057
external_id:
isi:
- '000956110300001'
pmid:
- '36883367'
intvolume: ' 62'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://uvadoc.uva.es/handle/10324/59798
month: '03'
oa: 1
oa_version: Submitted Version
page: 4625-4636
pmid: 1
publication: Inorganic Chemistry
publication_identifier:
eissn:
- 1520-510X
issn:
- 0020-1669
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage
metals
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2023'
...
---
_id: '12747'
abstract:
- lang: eng
text: Muscle degeneration is the most prevalent cause for frailty and dependency
in inherited diseases and ageing. Elucidation of pathophysiological mechanisms,
as well as effective treatments for muscle diseases, represents an important goal
in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine
cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency
in PCYT2 causes a severe disease with failure to thrive and progressive weakness.
pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the
participant phenotypes, with failure to thrive, progressive muscle weakness and
accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular
bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity
declines in ageing muscles of mice and humans, and adeno-associated virus-based
delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice,
offering a therapy for individuals with a rare disease and muscle ageing. Thus,
PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking
PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.
acknowledgement: 'The authors thank the participants and their families for participating
in the study. We thank all members of our laboratories for helpful discussions.
We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology
Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative
Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T.
Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy
of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A.
Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank
A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg,
Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul
D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector
Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson
(University of Iowa, Carver College of Medicine) for advice on muscle tissue handling.
We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment
of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry
of Education, Science and Research, the Austrian Academy of Sciences, and the City
of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z
271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program
(F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US
National Institutes of Health. C.K. is supported by a grant from the Agence Nationale
de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by
Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by
a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the
laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European
Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative
2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y.
acknowledge the support of the Spastic Paraplegia Foundation.'
article_processing_charge: No
article_type: original
author:
- first_name: Domagoj
full_name: Cikes, Domagoj
last_name: Cikes
- first_name: Kareem
full_name: Elsayad, Kareem
last_name: Elsayad
- first_name: Erdinc
full_name: Sezgin, Erdinc
last_name: Sezgin
- first_name: Erika
full_name: Koitai, Erika
last_name: Koitai
- first_name: Torma
full_name: Ferenc, Torma
last_name: Ferenc
- first_name: Michael
full_name: Orthofer, Michael
last_name: Orthofer
- first_name: Rebecca
full_name: Yarwood, Rebecca
last_name: Yarwood
- first_name: Leonhard X.
full_name: Heinz, Leonhard X.
last_name: Heinz
- first_name: Vitaly
full_name: Sedlyarov, Vitaly
last_name: Sedlyarov
- first_name: Nasser
full_name: Darwish-Miranda, Nasser
id: 39CD9926-F248-11E8-B48F-1D18A9856A87
last_name: Darwish-Miranda
orcid: 0000-0002-8821-8236
- first_name: Adrian
full_name: Taylor, Adrian
last_name: Taylor
- first_name: Sophie
full_name: Grapentine, Sophie
last_name: Grapentine
- first_name: Fathiya
full_name: al-Murshedi, Fathiya
last_name: al-Murshedi
- first_name: Anne
full_name: Abot, Anne
last_name: Abot
- first_name: Adelheid
full_name: Weidinger, Adelheid
last_name: Weidinger
- first_name: Candice
full_name: Kutchukian, Candice
last_name: Kutchukian
- first_name: Colline
full_name: Sanchez, Colline
last_name: Sanchez
- first_name: Shane J. F.
full_name: Cronin, Shane J. F.
last_name: Cronin
- first_name: Maria
full_name: Novatchkova, Maria
last_name: Novatchkova
- first_name: Anoop
full_name: Kavirayani, Anoop
last_name: Kavirayani
- first_name: Thomas
full_name: Schuetz, Thomas
last_name: Schuetz
- first_name: Bernhard
full_name: Haubner, Bernhard
last_name: Haubner
- first_name: Lisa
full_name: Haas, Lisa
last_name: Haas
- first_name: Astrid
full_name: Hagelkruys, Astrid
last_name: Hagelkruys
- first_name: Suzanne
full_name: Jackowski, Suzanne
last_name: Jackowski
- first_name: Andrey
full_name: Kozlov, Andrey
last_name: Kozlov
- first_name: Vincent
full_name: Jacquemond, Vincent
last_name: Jacquemond
- first_name: Claude
full_name: Knauf, Claude
last_name: Knauf
- first_name: Giulio
full_name: Superti-Furga, Giulio
last_name: Superti-Furga
- first_name: Eric
full_name: Rullman, Eric
last_name: Rullman
- first_name: Thomas
full_name: Gustafsson, Thomas
last_name: Gustafsson
- first_name: John
full_name: McDermot, John
last_name: McDermot
- first_name: Martin
full_name: Lowe, Martin
last_name: Lowe
- first_name: Zsolt
full_name: Radak, Zsolt
last_name: Radak
- first_name: Jeffrey S.
full_name: Chamberlain, Jeffrey S.
last_name: Chamberlain
- first_name: Marica
full_name: Bakovic, Marica
last_name: Bakovic
- first_name: Siddharth
full_name: Banka, Siddharth
last_name: Banka
- first_name: Josef M.
full_name: Penninger, Josef M.
last_name: Penninger
citation:
ama: Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is
critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515.
doi:10.1038/s42255-023-00766-2
apa: Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., …
Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle
health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2
chicago: Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc,
Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis
Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature,
2023. https://doi.org/10.1038/s42255-023-00766-2.
ieee: D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to
muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature,
pp. 495–515, 2023.
ista: Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz
LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot
A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani
A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond
V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak
Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid
biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.
mla: Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle
Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp.
495–515, doi:10.1038/s42255-023-00766-2.
short: D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood,
L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi,
A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova,
A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A.
Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson,
J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger,
Nature Metabolism 5 (2023) 495–515.
date_created: 2023-03-23T12:58:43Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2023-11-28T07:31:33Z
day: '20'
department:
- _id: Bio
doi: 10.1038/s42255-023-00766-2
external_id:
isi:
- '000992064000002'
pmid:
- '36941451'
intvolume: ' 5'
isi: 1
keyword:
- Cell Biology
- Physiology (medical)
- Endocrinology
- Diabetes and Metabolism
- Internal Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.03.02.482658
month: '03'
oa: 1
oa_version: Preprint
page: 495-515
pmid: 1
publication: Nature Metabolism
publication_identifier:
issn:
- 2522-5812
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s42255-023-00791-1
scopus_import: '1'
status: public
title: PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2023'
...
---
_id: '12756'
abstract:
- lang: eng
text: ESCRT-III family proteins form composite polymers that deform and cut membrane
tubes in the context of a wide range of cell biological processes across the tree
of life. In reconstituted systems, sequential changes in the composition of ESCRT-III
polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel
membranes. However, it is not known how composite ESCRT-III polymers are organized
and remodeled in space and time in a cellular context. Taking advantage of the
relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius,
one of the closest experimentally tractable prokaryotic relatives of eukaryotes,
we use super-resolution microscopy, electron microscopy, and computational modeling
to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III
division ring, which undergoes stepwise Vps4-dependent disassembly and contracts
to cut cells into two. These observations lead us to suggest sequential changes
in a patterned composite polymer as a general mechanism of ESCRT-III–dependent
membrane remodeling.
acknowledgement: "We thank Y. Liu and V. Hale for help with electron cryotomography;
the Medical Research Council (MRC) LMB Electron Microscopy Facility for access,
training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with
computing infrastructure. We also thank the Flow Cytometry Facility and the MRC
LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from
the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship:
ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P.
was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019).
B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the
VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and
a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346).
A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant no. 802960).
L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research
Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and
the Wellcome Trust (203276/Z/16/Z)."
article_number: eade5224
article_processing_charge: No
article_type: original
author:
- first_name: Fredrik
full_name: Hurtig, Fredrik
last_name: Hurtig
- first_name: Thomas C.Q.
full_name: Burgers, Thomas C.Q.
last_name: Burgers
- first_name: Alice
full_name: Cezanne, Alice
last_name: Cezanne
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Frank N.
full_name: Mol, Frank N.
last_name: Mol
- first_name: Jovan
full_name: Traparić, Jovan
last_name: Traparić
- first_name: Andre Arashiro
full_name: Pulschen, Andre Arashiro
last_name: Pulschen
- first_name: Tim
full_name: Nierhaus, Tim
last_name: Nierhaus
- first_name: Gabriel
full_name: Tarrason-Risa, Gabriel
last_name: Tarrason-Risa
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Jan
full_name: Löwe, Jan
last_name: Löwe
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rifka
full_name: Vlijm, Rifka
last_name: Vlijm
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
citation:
ama: Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise
Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell
division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224
apa: Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić,
J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly
of composite ESCRT-III polymers drives archaeal cell division. Science Advances.
American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224
chicago: Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank
N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly
and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives
Archaeal Cell Division.” Science Advances. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.
ieee: F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated
disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science
Advances, vol. 9, no. 11. American Association for the Advancement of Science,
2023.
ista: Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA,
Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum
B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.
mla: Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated
Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science
Advances, vol. 9, no. 11, eade5224, American Association for the Advancement
of Science, 2023, doi:10.1126/sciadv.ade5224.
short: F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A.
Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić,
R. Vlijm, B. Baum, Science Advances 9 (2023).
corr_author: '1'
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2025-04-23T08:50:02Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1126/sciadv.ade5224
ec_funded: 1
external_id:
isi:
- '000968083500010'
pmid:
- '36921039'
file:
- access_level: open_access
checksum: 6d7dbe9ed86a116c8a002d62971202c5
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:24:49Z
date_updated: 2023-03-27T06:24:49Z
file_id: '12768'
file_name: 2023_ScienceAdvances_Hurtig.pdf
file_size: 1826471
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:24:49Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2023'
...
---
_id: '12757'
abstract:
- lang: eng
text: My group and myself have studied respiratory complex I for almost 30 years,
starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics.
First breakthrough was the X-ray structure of the peripheral arm, followed by
structures of the membrane arm and finally the entire complex from Thermus thermophilus.
The developments in cryo-EM technology allowed us to solve the first complete
structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism
coupling, over large distances, the transfer of two electrons to pumping of four
protons across the membrane remained an enigma. Recently we have solved high-resolution
structures of mammalian and bacterial complex I under a range of redox conditions,
including catalytic turnover. This allowed us to propose a robust and universal
mechanism for complex I and related protein families. Redox reactions initially
drive conformational changes around the quinone cavity and a long-distance transfer
of substrate protons. These set up a stage for a series of electrostatically driven
proton transfers along the membrane arm (‘domino effect'), eventually resulting
in proton expulsion from the distal antiporter-like subunit. The mechanism radically
differs from previous suggestions, however, it naturally explains all the unusual
structural features of complex I. In this review I discuss the state of knowledge
on complex I, including the current most controversial issues.
article_processing_charge: No
article_type: review
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: 'Sazanov LA. From the “black box” to “domino effect” mechanism: What have we
learned from the structures of respiratory complex I. The Biochemical Journal.
2023;480(5):319-333. doi:10.1042/BCJ20210285'
apa: 'Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism:
What have we learned from the structures of respiratory complex I. The Biochemical
Journal. Portland Press. https://doi.org/10.1042/BCJ20210285'
chicago: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism:
What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.'
ieee: 'L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have
we learned from the structures of respiratory complex I,” The Biochemical Journal,
vol. 480, no. 5. Portland Press, pp. 319–333, 2023.'
ista: 'Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What
have we learned from the structures of respiratory complex I. The Biochemical
Journal. 480(5), 319–333.'
mla: 'Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What
Have We Learned from the Structures of Respiratory Complex I.” The Biochemical
Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.'
short: L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.
corr_author: '1'
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2024-10-09T21:04:50Z
day: '15'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1042/BCJ20210285
external_id:
isi:
- '000957065700001'
pmid:
- '36920092'
has_accepted_license: '1'
intvolume: ' 480'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1042/BCJ20210285
month: '03'
oa: 1
oa_version: Published Version
page: 319-333
pmid: 1
publication: The Biochemical Journal
publication_identifier:
eissn:
- 1470-8728
issn:
- 0264-6021
publication_status: published
publisher: Portland Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'From the ''black box'' to ''domino effect'' mechanism: What have we learned
from the structures of respiratory complex I'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 480
year: '2023'
...
---
_id: '12758'
abstract:
- lang: eng
text: AlphaFold changed the field of structural biology by achieving three-dimensional
(3D) structure prediction from protein sequence at experimental quality. The astounding
success even led to claims that the protein folding problem is “solved”. However,
protein folding problem is more than just structure prediction from sequence.
Presently, it is unknown if the AlphaFold-triggered revolution could help to solve
other problems related to protein folding. Here we assay the ability of AlphaFold
to predict the impact of single mutations on protein stability (ΔΔG) and function.
To study the question we extracted the pLDDT and metrics from AlphaFold
predictions before and after single mutation in a protein and correlated the predicted
change with the experimentally known ΔΔG values. Additionally, we correlated the
same AlphaFold pLDDT metrics with the impact of a single mutation on structure
using a large scale dataset of single mutations in GFP with the experimentally
assayed levels of fluorescence. We found a very weak or no correlation between
AlphaFold output metrics and change of protein stability or fluorescence. Our
results imply that AlphaFold may not be immediately applied to other problems
or applications in protein folding.
acknowledgement: The authors acknowledge the use of Zhores supercomputer [28] for
obtaining the results presented in this paper.The authors thank Zimin Foundation
and Petrovax for support of the presented study at the School of Molecular and Theoretical
Biology 2021.
article_number: e0282689
article_processing_charge: No
article_type: original
author:
- first_name: Marina A.
full_name: Pak, Marina A.
last_name: Pak
- first_name: Karina A.
full_name: Markhieva, Karina A.
last_name: Markhieva
- first_name: Mariia S.
full_name: Novikova, Mariia S.
last_name: Novikova
- first_name: Dmitry S.
full_name: Petrov, Dmitry S.
last_name: Petrov
- first_name: Ilya S.
full_name: Vorobyev, Ilya S.
last_name: Vorobyev
- first_name: Ekaterina
full_name: Maksimova, Ekaterina
id: 2FBE0DE4-F248-11E8-B48F-1D18A9856A87
last_name: Maksimova
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Dmitry N.
full_name: Ivankov, Dmitry N.
last_name: Ivankov
citation:
ama: Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. 2023;18(3).
doi:10.1371/journal.pone.0282689
apa: Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I.
S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0282689
chicago: Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov,
Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov.
“Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability
and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.
ieee: M. A. Pak et al., “Using AlphaFold to predict the impact of single
mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3.
Public Library of Science, 2023.
ista: Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov
F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations
on protein stability and function. PLoS ONE. 18(3), e0282689.
mla: Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations
on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689,
Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.
short: M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova,
F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-16T00:00:00Z
date_updated: 2025-04-23T08:50:30Z
day: '16'
ddc:
- '570'
department:
- _id: FyKo
- _id: MaRo
doi: 10.1371/journal.pone.0282689
external_id:
isi:
- '000985134400106'
pmid:
- '36928239'
file:
- access_level: open_access
checksum: 0281bdfccf8d76c4e08dd011c603f6b6
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T07:09:08Z
date_updated: 2023-03-27T07:09:08Z
file_id: '12771'
file_name: 2023_PLoSOne_Pak.pdf
file_size: 856625
relation: main_file
success: 1
file_date_updated: 2023-03-27T07:09:08Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using AlphaFold to predict the impact of single mutations on protein stability
and function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2023'
...
---
_id: '12759'
abstract:
- lang: eng
text: Stereological methods for estimating the 3D particle size and density from
2D projections are essential to many research fields. These methods are, however,
prone to errors arising from undetected particle profiles due to sectioning and
limited resolution, known as ‘lost caps’. A potential solution developed by Keiding,
Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for
lost caps by quantifying the smallest detectable profile in terms of its limiting
‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the
section surface. However, this simple solution has not been widely adopted nor
tested. Rather, model-independent design-based stereological methods, which do
not explicitly account for lost caps, have come to the fore. Here, we provide
the first experimental validation of the Keiding model by comparing the size and
density of particles estimated from 2D projections with direct measurement from
3D EM reconstructions of the same tissue. We applied the Keiding model to estimate
the size and density of somata, nuclei and vesicles in the cerebellum of mice
and rats, where high packing density can be problematic for design-based methods.
Our analysis reveals a Gaussian distribution for ϕ rather than a single value.
Nevertheless, curve fits of the Keiding model to the 2D diameter distribution
accurately estimate the mean ϕ and 3D diameter distribution. While systematic
testing using simulations revealed an upper limit to determining ϕ, our analysis
shows that estimated ϕ can be used to determine the 3D particle density from the
2D density under a wide range of conditions, and this method is potentially more
accurate than minimum-size-based lost-cap corrections and disector methods. Our
results show the Keiding model provides an efficient means of accurately estimating
the size and density of particles from 2D projections even under conditions of
a high density.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We thank the IST Austria Electron Microscopy Facility for technical
support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments
and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048;
224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal
Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung
der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z
312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding
from the European Research Council (ERC; https://erc.europa.eu) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692).
NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157)."
article_number: e0277148
article_processing_charge: No
article_type: original
author:
- first_name: Jason Seth
full_name: Rothman, Jason Seth
last_name: Rothman
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Noemi
full_name: Holderith, Noemi
last_name: Holderith
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: R.
full_name: Angus Silver, R.
last_name: Angus Silver
citation:
ama: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation
of a stereological method for estimating particle size and density from 2D projections
with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148
apa: Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus
Silver, R. (2023). Validation of a stereological method for estimating particle
size and density from 2D projections with high accuracy. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0277148
chicago: Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M
Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE.
Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.
ieee: J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus
Silver, “Validation of a stereological method for estimating particle size and
density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no.
3 March. Public Library of Science, 2023.
ista: Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023.
Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.
mla: Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating
Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE,
vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.
short: J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver,
PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2025-04-23T08:50:50Z
day: '17'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1371/journal.pone.0277148
ec_funded: 1
external_id:
isi:
- '001024737400001'
pmid:
- '36930689'
file:
- access_level: open_access
checksum: 2380331ec27cc87808826fc64419ac1c
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:51:09Z
date_updated: 2023-03-27T06:51:09Z
file_id: '12770'
file_name: 2023_PLoSOne_Rothman.pdf
file_size: 7290413
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:51:09Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: 3 March
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: V00739
name: Structural plasticity at mossy fiber-CA3 synapses
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Validation of a stereological method for estimating particle size and density
from 2D projections with high accuracy
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2023'
...
---
_id: '12760'
abstract:
- lang: eng
text: "Dynamic programming (DP) is one of the fundamental paradigms in algorithm
design. However,\r\nmany DP algorithms have to fill in large DP tables, represented
by two-dimensional arrays, which causes at least quadratic running times and space
usages. This has led to the development of improved algorithms for special cases
when the DPs satisfy additional properties like, e.g., the Monge property or total
monotonicity.\r\nIn this paper, we consider a new condition which assumes (among
some other technical assumptions) that the rows of the DP table are monotone.
Under this assumption, we introduce\r\na novel data structure for computing (1
+ ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting,
and with polylogarithmic update times when the DP entries change\r\ndynamically.
To the best of our knowledge, our new condition is incomparable to previous conditions
and is the first which allows to derive dynamic algorithms based on existing DPs.
Instead of using two-dimensional arrays to store the DP tables, we store the rows
of the DP tables using monotone piecewise constant functions. This allows us to
store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits,
and to perform operations, such as (min, +)-convolution or rounding, on these
functions in polylogarithmic time.\r\nWe further present several applications
of our data structure. For bicriteria versions of k-balanced graph partitioning
and simultaneous source location, we obtain the first dynamic algorithms with
subpolynomial update times, as well as the first static algorithms using only
near-linear time and space. Additionally, we obtain the currently fastest algorithm
for fully dynamic knapsack."
acknowledgement: "Monika Henzinger: This project has received funding from the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic
Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project
“Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional
funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research
is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA
project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science
Fund (FWF) project I 5025-N (DELTA), 2020-2024."
alternative_title:
- LIPIcs
article_number: '36'
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Stefan
full_name: Neumann, Stefan
last_name: Neumann
- first_name: Harald
full_name: Räcke, Harald
last_name: Räcke
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'Henzinger M, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone
dynamic programs and applications. In: 40th International Symposium on Theoretical
Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36'
apa: 'Henzinger, M., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic maintenance
of monotone dynamic programs and applications. In 40th International Symposium
on Theoretical Aspects of Computer Science (Vol. 254). Hamburg, Germany: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36'
chicago: Henzinger, Monika, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic
Maintenance of Monotone Dynamic Programs and Applications.” In 40th International
Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36.
ieee: M. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of
monotone dynamic programs and applications,” in 40th International Symposium
on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.
ista: 'Henzinger M, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone
dynamic programs and applications. 40th International Symposium on Theoretical
Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer
Science, LIPIcs, vol. 254, 36.'
mla: Henzinger, Monika, et al. “Dynamic Maintenance of Monotone Dynamic Programs
and Applications.” 40th International Symposium on Theoretical Aspects of Computer
Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.STACS.2023.36.
short: M. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium
on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023.
conference:
end_date: 2023-03-09
location: Hamburg, Germany
name: 'STACS: Symposium on Theoretical Aspects of Computer Science'
start_date: 2023-03-07
corr_author: '1'
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2025-09-09T12:22:44Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.STACS.2023.36
ec_funded: 1
external_id:
arxiv:
- '2301.01744'
isi:
- '001532693100036'
file:
- access_level: open_access
checksum: 22141ab8bc55188e2dfff665e5daecbd
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:37:22Z
date_updated: 2023-03-27T06:37:22Z
file_id: '12769'
file_name: 2023_LIPICS_HenzingerM.pdf
file_size: 872706
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:37:22Z
has_accepted_license: '1'
intvolume: ' 254'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: 40th International Symposium on Theoretical Aspects of Computer Science
publication_identifier:
isbn:
- '9783959772662'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic maintenance of monotone dynamic programs and applications
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 254
year: '2023'
...
---
_id: '12761'
abstract:
- lang: eng
text: "We consider the fluctuations of regular functions f of a Wigner matrix W
viewed as an entire matrix f (W). Going beyond the well-studied tracial mode,
Trf (W), which is equivalent to the customary linear statistics of eigenvalues,
we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic
matrix A. We identify three different and asymptotically independent modes of
this fluctuation, corresponding to the tracial part, the traceless diagonal part
and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find
that the off-diagonal modes fluctuate on a much smaller scale than the tracial
mode. As a main motivation to study CLT in such generality on small mesoscopic
scales, we determine\r\nthe fluctuations in the eigenstate thermalization hypothesis
(Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps
with any deterministic matrix are asymptotically Gaussian after a small spectral
averaging. Finally, in the macroscopic regime our result also generalizes (Zh.
Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover
ensembles in between. The main technical inputs are the recent\r\nmultiresolvent
local laws with traceless deterministic matrices from the companion paper (Comm.
Math. Phys. 388 (2021) 1005–1048)."
acknowledgement: The second author is partially funded by the ERC Advanced Grant “RMTBEYOND”
No. 101020331. The third author is supported by Dr. Max Rössler, the Walter Haefner
Foundation and the ETH Zürich Foundation.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Functional central limit theorems for Wigner
matrices. Annals of Applied Probability. 2023;33(1):447-489. doi:10.1214/22-AAP1820
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Functional central
limit theorems for Wigner matrices. Annals of Applied Probability. Institute
of Mathematical Statistics. https://doi.org/10.1214/22-AAP1820
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Functional Central
Limit Theorems for Wigner Matrices.” Annals of Applied Probability. Institute
of Mathematical Statistics, 2023. https://doi.org/10.1214/22-AAP1820.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Functional central limit theorems
for Wigner matrices,” Annals of Applied Probability, vol. 33, no. 1. Institute
of Mathematical Statistics, pp. 447–489, 2023.
ista: Cipolloni G, Erdös L, Schröder DJ. 2023. Functional central limit theorems
for Wigner matrices. Annals of Applied Probability. 33(1), 447–489.
mla: Cipolloni, Giorgio, et al. “Functional Central Limit Theorems for Wigner Matrices.”
Annals of Applied Probability, vol. 33, no. 1, Institute of Mathematical
Statistics, 2023, pp. 447–89, doi:10.1214/22-AAP1820.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Applied Probability 33 (2023)
447–489.
corr_author: '1'
date_created: 2023-03-26T22:01:08Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2025-04-14T07:57:19Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/22-AAP1820
ec_funded: 1
external_id:
arxiv:
- '2012.13218'
isi:
- '000946432400015'
intvolume: ' 33'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2012.13218
month: '02'
oa: 1
oa_version: Preprint
page: 447-489
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Annals of Applied Probability
publication_identifier:
issn:
- 1050-5164
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Functional central limit theorems for Wigner matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2023'
...
---
_id: '12762'
abstract:
- lang: eng
text: Neurons in the brain are wired into adaptive networks that exhibit collective
dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches.
Although existing models account for oscillations and avalanches separately, they
typically do not explain both phenomena, are too complex to analyze analytically
or intractable to infer from data rigorously. Here we propose a feedback-driven
Ising-like class of neural networks that captures avalanches and oscillations
simultaneously and quantitatively. In the simplest yet fully microscopic model
version, we can analytically compute the phase diagram and make direct contact
with human brain resting-state activity recordings via tractable inference of
the model’s two essential parameters. The inferred model quantitatively captures
the dynamics over a broad range of scales, from single sensor oscillations to
collective behaviors of extreme events and neuronal avalanches. Importantly, the
inferred parameters indicate that the co-existence of scale-specific (oscillations)
and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical
point at the onset of self-sustained oscillations.
acknowledgement: This research was funded in whole, or in part, by the Austrian Science
Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose
of open access, the author has applied a CC BY public copyright licence to any Author
Accepted Manuscript version arising from this submission. The study was supported
by the European Union Horizon 2020 research and innovation program under the Marie
Sklodowska-Curie action (grant agreement No. 754411 to F.L.).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Selver
full_name: Pepic, Selver
id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425
last_name: Pepic
- first_name: Oren
full_name: Shriki, Oren
last_name: Shriki
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9
apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023).
Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain. Nature Computational Science.
Springer Nature. https://doi.org/10.1038/s43588-023-00410-9
chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele
De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence
of Avalanches and Oscillations in Resting Human Brain.” Nature Computational
Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.
ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical
modeling of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain,” Nature Computational Science, vol. 3. Springer
Nature, pp. 254–263, 2023.
ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling
of adaptive neural networks explains co-existence of avalanches and oscillations
in resting human brain. Nature Computational Science. 3, 254–263.
mla: Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks
Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.”
Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63,
doi:10.1038/s43588-023-00410-9.
short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational
Science 3 (2023) 254–263.
corr_author: '1'
date_created: 2023-03-26T22:01:08Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2025-09-09T12:23:42Z
day: '20'
ddc:
- '570'
department:
- _id: GaTk
- _id: GradSch
doi: 10.1038/s43588-023-00410-9
ec_funded: 1
external_id:
arxiv:
- '2108.06686'
isi:
- '000968161800002'
pmid:
- '38177880'
file:
- access_level: open_access
checksum: 7c63b2b2edfd68aaffe96d70ca6a865a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T12:39:57Z
date_updated: 2023-08-16T12:39:57Z
file_id: '14073'
file_name: 2023_NatureCompScience_Lombardi.pdf
file_size: 4474284
relation: main_file
success: 1
file_date_updated: 2023-08-16T12:39:57Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 254-263
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: eb943429-77a9-11ec-83b8-9f471cdf5c67
grant_number: M03318
name: Functional Advantages of Critical Brain Dynamics
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication: Nature Computational Science
publication_identifier:
eissn:
- 2662-8457
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Statistical modeling of adaptive neural networks explains co-existence of avalanches
and oscillations in resting human brain
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 3
year: '2023'
...
---
_id: '12763'
abstract:
- lang: eng
text: 'Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift
176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended
the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets
S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert
showed that sets of positive reach in Euclidean space and Riemannian manifolds
are very similar. In this paper we introduce a slight variant of Kleinjohann’s
and Bangert’s extension and quantify the similarity between sets of positive reach
in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we
bound the local feature size (a local version of the reach) of its lifting to
the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that
rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated
by the importance of the reach and local feature size to manifold learning, topological
inference, and triangulating manifolds and the fact that intrinsic approaches
circumvent the curse of dimensionality.'
acknowledgement: "We thank Eddie Aamari, David Cohen-Steiner, Isa Costantini, Fred
Chazal, Ramsay Dyer, André Lieutier, and Alef Sterk for discussion and Pierre Pansu
for encouragement. We further acknowledge the anonymous reviewers whose comments
helped improve the exposition.\r\nThe research leading to these results has received
funding from the European Research Council (ERC) under the European Union’s Seventh
Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic
Foundations of Geometry Understanding in Higher Dimensions). The first author is
further supported by the French government, through the 3IA Côte d’Azur Investments
in the Future project managed by the National Research Agency (ANR) with the reference
number ANR-19-P3IA-0002. The second author is supported by the European Union’s
Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
Grant Agreement No. 754411 and the Austrian science fund (FWF) M-3073."
article_processing_charge: No
article_type: original
author:
- first_name: Jean Daniel
full_name: Boissonnat, Jean Daniel
last_name: Boissonnat
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Boissonnat JD, Wintraecken M. The reach of subsets of manifolds. Journal
of Applied and Computational Topology. 2023;7:619-641. doi:10.1007/s41468-023-00116-x
apa: Boissonnat, J. D., & Wintraecken, M. (2023). The reach of subsets of manifolds.
Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-023-00116-x
chicago: Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets
of Manifolds.” Journal of Applied and Computational Topology. Springer
Nature, 2023. https://doi.org/10.1007/s41468-023-00116-x.
ieee: J. D. Boissonnat and M. Wintraecken, “The reach of subsets of manifolds,”
Journal of Applied and Computational Topology, vol. 7. Springer Nature,
pp. 619–641, 2023.
ista: Boissonnat JD, Wintraecken M. 2023. The reach of subsets of manifolds. Journal
of Applied and Computational Topology. 7, 619–641.
mla: Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of
Manifolds.” Journal of Applied and Computational Topology, vol. 7, Springer
Nature, 2023, pp. 619–41, doi:10.1007/s41468-023-00116-x.
short: J.D. Boissonnat, M. Wintraecken, Journal of Applied and Computational Topology
7 (2023) 619–641.
corr_author: '1'
date_created: 2023-03-26T22:01:08Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2025-04-14T07:44:01Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s41468-023-00116-x
ec_funded: 1
intvolume: ' 7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://inserm.hal.science/INRIA-SACLAY/hal-04083524v1
month: '09'
oa: 1
oa_version: Submitted Version
page: 619-641
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: fc390959-9c52-11eb-aca3-afa58bd282b2
grant_number: M03073
name: Learning and triangulating manifolds via collapses
publication: Journal of Applied and Computational Topology
publication_identifier:
eissn:
- 2367-1734
issn:
- 2367-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The reach of subsets of manifolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '12764'
abstract:
- lang: eng
text: We study a new discretization of the Gaussian curvature for polyhedral surfaces.
This discrete Gaussian curvature is defined on each conical singularity of a polyhedral
surface as the quotient of the angle defect and the area of the Voronoi cell corresponding
to the singularity. We divide polyhedral surfaces into discrete conformal classes
using a generalization of discrete conformal equivalence pioneered by Feng Luo.
We subsequently show that, in every discrete conformal class, there exists a polyhedral
surface with constant discrete Gaussian curvature. We also provide explicit examples
to demonstrate that this surface is in general not unique.
acknowledgement: Open access funding provided by the Austrian Science Fund (FWF).
This research was supported by the FWF grant, Project number I4245-N35, and by the
Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) - Project-ID
195170736 - TRR109.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hana
full_name: Kourimska, Hana
id: D9B8E14C-3C26-11EA-98F5-1F833DDC885E
last_name: Kourimska
orcid: 0000-0001-7841-0091
citation:
ama: Kourimska H. Discrete yamabe problem for polyhedral surfaces. Discrete and
Computational Geometry. 2023;70:123-153. doi:10.1007/s00454-023-00484-2
apa: Kourimska, H. (2023). Discrete yamabe problem for polyhedral surfaces. Discrete
and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00484-2
chicago: Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” Discrete
and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00484-2.
ieee: H. Kourimska, “Discrete yamabe problem for polyhedral surfaces,” Discrete
and Computational Geometry, vol. 70. Springer Nature, pp. 123–153, 2023.
ista: Kourimska H. 2023. Discrete yamabe problem for polyhedral surfaces. Discrete
and Computational Geometry. 70, 123–153.
mla: Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” Discrete
and Computational Geometry, vol. 70, Springer Nature, 2023, pp. 123–53, doi:10.1007/s00454-023-00484-2.
short: H. Kourimska, Discrete and Computational Geometry 70 (2023) 123–153.
corr_author: '1'
date_created: 2023-03-26T22:01:09Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2025-04-23T08:59:15Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s00454-023-00484-2
external_id:
isi:
- '000948148000001'
pmid:
- '37292248'
file:
- access_level: open_access
checksum: cdbf90ba4a7ddcb190d37b9e9d4cb9d3
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T11:46:24Z
date_updated: 2023-10-04T11:46:24Z
file_id: '14396'
file_name: 2023_DiscreteGeometry_Kourimska.pdf
file_size: 1026683
relation: main_file
success: 1
file_date_updated: 2023-10-04T11:46:24Z
has_accepted_license: '1'
intvolume: ' 70'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 123-153
pmid: 1
project:
- _id: 26AD5D90-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I04245
name: Algebraic Footprints of Geometric Features in Homology
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Discrete yamabe problem for polyhedral surfaces
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2023'
...
---
OA_place: repository
OA_type: green
_id: '12765'
abstract:
- lang: eng
text: "Animals exhibit a variety of behavioural defences against socially transmitted
parasites. These defences evolved to increase host fitness by avoiding, resisting
or tolerating infection.\r\nBecause they can occur in both infected individuals
and their uninfected social partners, these defences often have important consequences
for the social group.\r\nHere, we discuss the evolution and ecology of anti-parasite
behavioural defences across a taxonomically wide social spectrum, considering
colonial groups, stable groups, transitional groups and solitary animals.\r\nWe
discuss avoidance, resistance and tolerance behaviours across these social group
structures, identifying how social complexity, group composition and interdependent
social relationships may contribute to the expression and evolution of behavioural
strategies.\r\nFinally, we outline avenues for further investigation such as approaches
to quantify group-level responses, and the connection of the physiological and
behavioural response to parasites in different social contexts."
article_processing_charge: No
article_type: review
author:
- first_name: Sebastian
full_name: Stockmaier, Sebastian
last_name: Stockmaier
- first_name: Yuko
full_name: Ulrich, Yuko
last_name: Ulrich
- first_name: Gregory F.
full_name: Albery, Gregory F.
last_name: Albery
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Patricia C.
full_name: Lopes, Patricia C.
last_name: Lopes
citation:
ama: Stockmaier S, Ulrich Y, Albery GF, Cremer S, Lopes PC. Behavioural defences
against parasites across host social structures. Functional Ecology. 2023;37(4):809-820.
doi:10.1111/1365-2435.14310
apa: Stockmaier, S., Ulrich, Y., Albery, G. F., Cremer, S., & Lopes, P. C. (2023).
Behavioural defences against parasites across host social structures. Functional
Ecology. British Ecological Society. https://doi.org/10.1111/1365-2435.14310
chicago: Stockmaier, Sebastian, Yuko Ulrich, Gregory F. Albery, Sylvia Cremer, and
Patricia C. Lopes. “Behavioural Defences against Parasites across Host Social
Structures.” Functional Ecology. British Ecological Society, 2023. https://doi.org/10.1111/1365-2435.14310.
ieee: S. Stockmaier, Y. Ulrich, G. F. Albery, S. Cremer, and P. C. Lopes, “Behavioural
defences against parasites across host social structures,” Functional Ecology,
vol. 37, no. 4. British Ecological Society, pp. 809–820, 2023.
ista: Stockmaier S, Ulrich Y, Albery GF, Cremer S, Lopes PC. 2023. Behavioural defences
against parasites across host social structures. Functional Ecology. 37(4), 809–820.
mla: Stockmaier, Sebastian, et al. “Behavioural Defences against Parasites across
Host Social Structures.” Functional Ecology, vol. 37, no. 4, British Ecological
Society, 2023, pp. 809–20, doi:10.1111/1365-2435.14310.
short: S. Stockmaier, Y. Ulrich, G.F. Albery, S. Cremer, P.C. Lopes, Functional
Ecology 37 (2023) 809–820.
date_created: 2023-03-26T22:01:09Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2025-07-10T11:50:31Z
day: '01'
department:
- _id: SyCr
doi: 10.1111/1365-2435.14310
external_id:
isi:
- '000948940500001'
intvolume: ' 37'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://digitalcommons.chapman.edu/cgi/viewcontent.cgi?article=1585&context=sees_articles
month: '04'
oa: 1
oa_version: Submitted Version
page: 809-820
publication: Functional Ecology
publication_identifier:
eissn:
- 1365-2435
issn:
- 0269-8463
publication_status: published
publisher: British Ecological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Behavioural defences against parasites across host social structures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '12786'
abstract:
- lang: eng
text: AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout
the brain. Their signalling is uniquely diversified by brain region-specific auxiliary
subunits, providing an opportunity for the development of selective therapeutics.
AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets
of emerging anti-epileptic drugs. To understand their therapeutic activity, we
determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three
potent, chemically diverse ligands. We find that despite sharing a lipid-exposed
and water-accessible binding pocket, drug action is differentially affected by
binding-site mutants. Together with patch-clamp recordings and MD simulations
we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface
contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally,
negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing
AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate
the action of TARPs, demonstrate the sensitive balance between positive and negative
modulatory action, and provide a mechanistic platform for development of both
positive and negative selective AMPAR modulators.
acknowledgement: We thank James Krieger for generating the ‘proDy’ interaction maps
in Fig. 5B and S7C, and Jan-Niklas Dohrke for critically reading the manuscript.
We thank members of the Greger lab for insightful comments during this study. We
acknowledge Trevor Rutherford for confirming ligand integrity by NMR. We are also
grateful to LMB scientific computing and the EM facility for their support. This
research was funded in part by the Wellcome Trust (223194/Z/21/Z) to I.H.G. For
the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied
a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version
arising from this submission. Further funding came from the Medical Research Council
(MRU105174197) to I.H.G, and NIH grant (R56/R01MH123474) to T.N.
article_number: '1659'
article_processing_charge: No
article_type: original
author:
- first_name: Danyang
full_name: Zhang, Danyang
last_name: Zhang
- first_name: Remigijus
full_name: Lape, Remigijus
last_name: Lape
- first_name: Saher A.
full_name: Shaikh, Saher A.
last_name: Shaikh
- first_name: Bianka K.
full_name: Kohegyi, Bianka K.
last_name: Kohegyi
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Ondrej
full_name: Cais, Ondrej
last_name: Cais
- first_name: Terunaga
full_name: Nakagawa, Terunaga
last_name: Nakagawa
- first_name: Ingo H.
full_name: Greger, Ingo H.
last_name: Greger
citation:
ama: Zhang D, Lape R, Shaikh SA, et al. Modulatory mechanisms of TARP γ8-selective
AMPA receptor therapeutics. Nature Communications. 2023;14. doi:10.1038/s41467-023-37259-5
apa: Zhang, D., Lape, R., Shaikh, S. A., Kohegyi, B. K., Watson, J., Cais, O., …
Greger, I. H. (2023). Modulatory mechanisms of TARP γ8-selective AMPA receptor
therapeutics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37259-5
chicago: Zhang, Danyang, Remigijus Lape, Saher A. Shaikh, Bianka K. Kohegyi, Jake
Watson, Ondrej Cais, Terunaga Nakagawa, and Ingo H. Greger. “Modulatory Mechanisms
of TARP Γ8-Selective AMPA Receptor Therapeutics.” Nature Communications.
Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37259-5.
ieee: D. Zhang et al., “Modulatory mechanisms of TARP γ8-selective AMPA receptor
therapeutics,” Nature Communications, vol. 14. Springer Nature, 2023.
ista: Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson J, Cais O, Nakagawa T, Greger
IH. 2023. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics.
Nature Communications. 14, 1659.
mla: Zhang, Danyang, et al. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor
Therapeutics.” Nature Communications, vol. 14, 1659, Springer Nature, 2023,
doi:10.1038/s41467-023-37259-5.
short: D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa,
I.H. Greger, Nature Communications 14 (2023).
date_created: 2023-04-02T22:01:09Z
date_published: 2023-03-25T00:00:00Z
date_updated: 2023-12-13T11:15:58Z
day: '25'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41467-023-37259-5
external_id:
isi:
- '001066658700003'
file:
- access_level: open_access
checksum: 0a97b31191432dae5853bbb5ccb7698d
content_type: application/pdf
creator: dernst
date_created: 2023-04-03T06:38:56Z
date_updated: 2023-04-03T06:38:56Z
file_id: '12797'
file_name: 2023_NatureComm_Zhang.pdf
file_size: 2613996
relation: main_file
success: 1
file_date_updated: 2023-04-03T06:38:56Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '12789'
abstract:
- lang: eng
text: Experiments have shown that charge distributions of granular materials are
non-Gaussian, with broad tails that indicate many particles with high charge.
This observation has consequences for the behavior of granular materials in many
settings, and may bear relevance to the underlying charge transfer mechanism.
However, there is the unaddressed possibility that broad tails arise due to experimental
uncertainties, as determining the shapes of tails is nontrivial. Here we show
that measurement uncertainties can indeed account for most of the tail broadening
previously observed. The clue that reveals this is that distributions are sensitive
to the electric field at which they are measured; ones measured at low (high)
fields have larger (smaller) tails. Accounting for sources of uncertainty, we
reproduce this broadening in silico. Finally, we use our results to back out the
true charge distribution without broadening, which we find is still non-Guassian,
though with substantially different behavior at the tails and indicating significantly
fewer highly charged particles. These results have implications in many natural
settings where electrostatic interactions, especially among highly charged particles,
strongly affect granular behavior.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This research was supported by Grants QUIMAL 160001 and Fondecyt
1221597. This project has received funding from the European Research Council (ERC)
under the European Union's Horizon 2020 research and innovation programme (Grant
Agreement No. 949120). This research was supported by the Scientific Service Units
of The Institute of Science and Technology Austria (ISTA) through resources provided
by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo
Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.
article_number: '034901'
article_processing_charge: No
article_type: original
author:
- first_name: Nicolás
full_name: Mujica, Nicolás
last_name: Mujica
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular
charge distributions. Physical Review E. 2023;107(3). doi:10.1103/PhysRevE.107.034901
apa: Mujica, N., & Waitukaitis, S. R. (2023). Accurate determination of the
shapes of granular charge distributions. Physical Review E. American Physical
Society. https://doi.org/10.1103/PhysRevE.107.034901
chicago: Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the
Shapes of Granular Charge Distributions.” Physical Review E. American Physical
Society, 2023. https://doi.org/10.1103/PhysRevE.107.034901.
ieee: N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of
granular charge distributions,” Physical Review E, vol. 107, no. 3. American
Physical Society, 2023.
ista: Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular
charge distributions. Physical Review E. 107(3), 034901.
mla: Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes
of Granular Charge Distributions.” Physical Review E, vol. 107, no. 3,
034901, American Physical Society, 2023, doi:10.1103/PhysRevE.107.034901.
short: N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).
corr_author: '1'
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2025-04-14T07:54:10Z
day: '01'
ddc:
- '530'
department:
- _id: ScWa
doi: 10.1103/PhysRevE.107.034901
ec_funded: 1
external_id:
isi:
- '000992142700001'
pmid:
- '37072968'
file:
- access_level: open_access
checksum: 48f5dfe4e5f1c46c3c86805cd8f84bea
content_type: application/pdf
creator: swaituka
date_created: 2023-11-27T09:51:48Z
date_updated: 2023-11-27T09:51:48Z
file_id: '14612'
file_name: PhysRevE.107.034901 (1).pdf
file_size: 1428631
relation: main_file
success: 1
file_date_updated: 2023-11-27T09:51:48Z
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa
call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication: Physical Review E
publication_identifier:
eissn:
- 2470-0053
issn:
- 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accurate determination of the shapes of granular charge distributions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 107
year: '2023'
...
---
_id: '12790'
abstract:
- lang: eng
text: Motivated by the recent discoveries of superconductivity in bilayer and trilayer
graphene, we theoretically investigate superconductivity and other interaction-driven
phases in multilayer graphene stacks. To this end, we study the density of states
of multilayer graphene with up to four layers at the single-particle band structure
level in the presence of a transverse electric field. Among the considered structures,
tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density
of states. We study the phases that can arise in ABCA graphene by tuning the carrier
density and transverse electric field. For a broad region of the tuning parameters,
the presence of strong Coulomb repulsion leads to a spontaneous spin and valley
symmetry breaking via Stoner transitions. Using a model that incorporates the
spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism
for superconductivity driven by repulsive Coulomb interactions. We find that the
strongest superconducting instability is in the p-wave channel, and occurs in
proximity to the onset of Stoner transitions. Interestingly, we find a range of
densities and transverse electric fields where superconductivity develops out
of a strongly corrugated, singly connected Fermi surface in each valley, leading
to a topologically nontrivial chiral p+ip superconducting state with an even number
of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked
tetralayer graphene as a promising platform for observing strongly correlated
physics and topological superconductivity.
acknowledgement: E.B. and T.H. were supported by the European Research Council (ERC)
under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science
Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.
article_number: '104502'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Tobias
full_name: Holder, Tobias
last_name: Holder
- first_name: Erez
full_name: Berg, Erez
last_name: Berg
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform
for interaction-driven physics and topological superconductivity. Physical
Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502
apa: Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes
as a platform for interaction-driven physics and topological superconductivity.
Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502
chicago: Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer
Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.”
Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502.
ieee: A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as
a platform for interaction-driven physics and topological superconductivity,”
Physical Review B, vol. 107, no. 10. American Physical Society, 2023.
ista: Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform
for interaction-driven physics and topological superconductivity. Physical Review
B. 107(10), 104502.
mla: Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven
Physics and Topological Superconductivity.” Physical Review B, vol. 107,
no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.
short: A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).
date_created: 2023-04-02T22:01:10Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-01T13:59:29Z
day: '01'
department:
- _id: MaSe
- _id: MiLe
doi: 10.1103/PhysRevB.107.104502
external_id:
arxiv:
- '2211.02492'
isi:
- '000945526400003'
intvolume: ' 107'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.02492
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/
scopus_import: '1'
status: public
title: Multilayer graphenes as a platform for interaction-driven physics and topological
superconductivity
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12791'
abstract:
- lang: eng
text: We investigate the capabilities of Physics-Informed Neural Networks (PINNs)
to reconstruct turbulent Rayleigh–Bénard flows using only temperature information.
We perform a quantitative analysis of the quality of the reconstructions at various
amounts of low-passed-filtered information and turbulent intensities. We compare
our results with those obtained via nudging, a classical equation-informed data
assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct
with high precision, comparable to the one achieved with nudging. At high Rayleigh
numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction
of the velocity fields only when data for temperature is provided with high spatial
and temporal density. When data becomes sparse, the PINNs performance worsens,
not only in a point-to-point error sense but also, and contrary to nudging, in
a statistical sense, as can be seen in the probability density functions and energy
spectra.
acknowledgement: This project has received partial funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme
(Grant Agreement No. 882340))
article_number: '16'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Patricio
full_name: Clark Di Leoni, Patricio
last_name: Clark Di Leoni
- first_name: Lokahith N
full_name: Agasthya, Lokahith N
id: cd100965-0804-11ed-9c55-f4878ff4e877
last_name: Agasthya
- first_name: Michele
full_name: Buzzicotti, Michele
last_name: Buzzicotti
- first_name: Luca
full_name: Biferale, Luca
last_name: Biferale
citation:
ama: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard
flows out of temperature-only measurements using Physics-Informed Neural Networks.
The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9
apa: Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023).
Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using
Physics-Informed Neural Networks. The European Physical Journal E. Springer
Nature. https://doi.org/10.1140/epje/s10189-023-00276-9
chicago: Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and
Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements
Using Physics-Informed Neural Networks.” The European Physical Journal E.
Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9.
ieee: P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing
Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed
Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer
Nature, 2023.
ista: Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing
Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed
Neural Networks. The European Physical Journal E. 46(3), 16.
mla: Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out
of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The
European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9.
short: P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European
Physical Journal E 46 (2023).
date_created: 2023-04-02T22:01:11Z
date_published: 2023-03-20T00:00:00Z
date_updated: 2025-04-23T08:52:35Z
day: '20'
department:
- _id: CaMu
doi: 10.1140/epje/s10189-023-00276-9
external_id:
arxiv:
- '2301.07769'
isi:
- '000956387200001'
pmid:
- '36939938'
intvolume: ' 46'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2301.07769'
month: '03'
oa: 1
oa_version: Preprint
pmid: 1
publication: The European Physical Journal E
publication_identifier:
eissn:
- 1292-895X
issn:
- 1292-8941
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using
Physics-Informed Neural Networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2023'
...
---
_id: '12792'
abstract:
- lang: eng
text: In the physics literature the spectral form factor (SFF), the squared Fourier
transform of the empirical eigenvalue density, is the most common tool to test
universality for disordered quantum systems, yet previous mathematical results
have been restricted only to two exactly solvable models (Forrester in J Stat
Phys 183:33, 2021. https://doi.org/10.1007/s10955-021-02767-5, Commun Math Phys
387:215–235, 2021. https://doi.org/10.1007/s00220-021-04193-w). We rigorously
prove the physics prediction on SFF up to an intermediate time scale for a large
class of random matrices using a robust method, the multi-resolvent local laws.
Beyond Wigner matrices we also consider the monoparametric ensemble and prove
that universality of SFF can already be triggered by a single random parameter,
supplementing the recently proven Wigner–Dyson universality (Cipolloni et al.
in Probab Theory Relat Fields, 2021. https://doi.org/10.1007/s00440-022-01156-7)
to larger spectral scales. Remarkably, extensive numerics indicates that our formulas
correctly predict the SFF in the entire slope-dip-ramp regime, as customarily
called in physics.
acknowledgement: "We are grateful to the authors of [25] for sharing with us their
insights and preliminary numerical results. We are especially thankful to Stephen
Shenker for very valuable advice over several email communications. Helpful comments
on the manuscript from Peter Forrester and from the anonymous referees are also
acknowledged.\r\nOpen access funding provided by Institute of Science and Technology
(IST Austria).\r\nLászló Erdős: Partially supported by ERC Advanced Grant \"RMTBeyond\"
No. 101020331. Dominik Schröder: Supported by Dr. Max Rössler, the Walter Haefner
Foundation and the ETH Zürich Foundation."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. On the spectral form factor for random matrices.
Communications in Mathematical Physics. 2023;401:1665-1700. doi:10.1007/s00220-023-04692-y
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). On the spectral form
factor for random matrices. Communications in Mathematical Physics. Springer
Nature. https://doi.org/10.1007/s00220-023-04692-y
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “On the Spectral
Form Factor for Random Matrices.” Communications in Mathematical Physics.
Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04692-y.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “On the spectral form factor for
random matrices,” Communications in Mathematical Physics, vol. 401. Springer
Nature, pp. 1665–1700, 2023.
ista: Cipolloni G, Erdös L, Schröder DJ. 2023. On the spectral form factor for random
matrices. Communications in Mathematical Physics. 401, 1665–1700.
mla: Cipolloni, Giorgio, et al. “On the Spectral Form Factor for Random Matrices.”
Communications in Mathematical Physics, vol. 401, Springer Nature, 2023,
pp. 1665–700, doi:10.1007/s00220-023-04692-y.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics
401 (2023) 1665–1700.
corr_author: '1'
date_created: 2023-04-02T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2025-04-14T07:57:19Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00220-023-04692-y
ec_funded: 1
external_id:
isi:
- '000957343500001'
file:
- access_level: open_access
checksum: 72057940f76654050ca84a221f21786c
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T12:09:18Z
date_updated: 2023-10-04T12:09:18Z
file_id: '14397'
file_name: 2023_CommMathPhysics_Cipolloni.pdf
file_size: 859967
relation: main_file
success: 1
file_date_updated: 2023-10-04T12:09:18Z
has_accepted_license: '1'
intvolume: ' 401'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1665-1700
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the spectral form factor for random matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 401
year: '2023'
...
---
_id: '12818'
abstract:
- lang: eng
text: The multicellular organization of diverse systems, including embryos, intestines,
and tumors relies on coordinated cell migration in curved environments. In these
settings, cells establish supracellular patterns of motion, including collective
rotation and invasion. While such collective modes have been studied extensively
in flat systems, the consequences of geometrical and topological constraints on
collective migration in curved systems are largely unknown. Here, we discover
a collective mode of cell migration in rotating spherical tissues manifesting
as a propagating single-wavelength velocity wave. This wave is accompanied by
an apparently incompressible supracellular flow pattern featuring topological
defects as dictated by the spherical topology. Using a minimal active particle
model, we reveal that this collective mode arises from the effect of curvature
on the active flocking behavior of a cell layer confined to a spherical surface.
Our results thus identify curvature-induced velocity waves as a mode of collective
cell migration, impacting the dynamical organization of 3D curved tissues.
acknowledgement: We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti,
and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B.
is a NOMIS fellow supported by the NOMIS foundation and was in part supported by
a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM)
and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science
Program (LT000475/2018-C) and from the National Science Foundation, through the
Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support
from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open
Access funding enabled and organized by Projekt DEAL.
article_number: '1643'
article_processing_charge: No
article_type: original
author:
- first_name: Tom
full_name: Brandstätter, Tom
last_name: Brandstätter
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Yu Long
full_name: Han, Yu Long
last_name: Han
- first_name: Ricard
full_name: Alert, Ricard
last_name: Alert
- first_name: Ming
full_name: Guo, Ming
last_name: Guo
- first_name: Chase P.
full_name: Broedersz, Chase P.
last_name: Broedersz
citation:
ama: Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature
induces active velocity waves in rotating spherical tissues. Nature Communications.
2023;14. doi:10.1038/s41467-023-37054-2
apa: Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz,
C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues.
Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2
chicago: Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo,
and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical
Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2.
ieee: T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz,
“Curvature induces active velocity waves in rotating spherical tissues,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature
induces active velocity waves in rotating spherical tissues. Nature Communications.
14, 1643.
mla: Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating
Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature,
2023, doi:10.1038/s41467-023-37054-2.
short: T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz,
Nature Communications 14 (2023).
date_created: 2023-04-09T22:01:00Z
date_published: 2023-03-24T00:00:00Z
date_updated: 2023-08-01T14:05:30Z
day: '24'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1038/s41467-023-37054-2
external_id:
isi:
- '000959887700008'
pmid:
- '36964141'
file:
- access_level: open_access
checksum: 54f06f9eee11d43bab253f3492c983ba
content_type: application/pdf
creator: dernst
date_created: 2023-04-11T06:27:00Z
date_updated: 2023-04-11T06:27:00Z
file_id: '12821'
file_name: 2023_NatureComm_Brandstaetter.pdf
file_size: 4146777
relation: main_file
success: 1
file_date_updated: 2023-04-11T06:27:00Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Curvature induces active velocity waves in rotating spherical tissues
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12819'
abstract:
- lang: eng
text: 'Reaching a high cavity population with a coherent pump in the strong-coupling
regime of a single-atom laser is impossible due to the photon blockade effect.
In this Letter, we experimentally demonstrate that in a single-atom maser based
on a transmon strongly coupled to two resonators, it is possible to pump over
a dozen photons into the system. The first high-quality resonator plays the role
of a usual lasing cavity, and the second one presents a controlled dissipation
channel, bolstering population inversion, and modifies the energy-level structure
to lift the blockade. As confirmation of the lasing action, we observe conventional
laser features such as a narrowing of the emission linewidth and external signal
amplification. Additionally, we report unique single-atom features: self-quenching
and several lasing thresholds.'
acknowledgement: We thank N.N. Abramov for assistance with the experimental setup.
The sample was fabricated using equipment of MIPT Shared Facilities Center. This
research was supported by Russian Science Foundation, grant no. 21-72-30026.
article_number: L031701
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Alesya
full_name: Sokolova, Alesya
id: 2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a
last_name: Sokolova
orcid: 0000-0002-8308-4144
- first_name: D. A.
full_name: Kalacheva, D. A.
last_name: Kalacheva
- first_name: G. P.
full_name: Fedorov, G. P.
last_name: Fedorov
- first_name: O. V.
full_name: Astafiev, O. V.
last_name: Astafiev
citation:
ama: Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade
in a circuit-QED single-atom maser with engineered metastability and strong coupling.
Physical Review A. 2023;107(3). doi:10.1103/PhysRevA.107.L031701
apa: Sokolova, A., Kalacheva, D. A., Fedorov, G. P., & Astafiev, O. V. (2023).
Overcoming photon blockade in a circuit-QED single-atom maser with engineered
metastability and strong coupling. Physical Review A. American Physical
Society. https://doi.org/10.1103/PhysRevA.107.L031701
chicago: Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming
Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability
and Strong Coupling.” Physical Review A. American Physical Society, 2023.
https://doi.org/10.1103/PhysRevA.107.L031701.
ieee: A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming
photon blockade in a circuit-QED single-atom maser with engineered metastability
and strong coupling,” Physical Review A, vol. 107, no. 3. American Physical
Society, 2023.
ista: Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon
blockade in a circuit-QED single-atom maser with engineered metastability and
strong coupling. Physical Review A. 107(3), L031701.
mla: Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom
Maser with Engineered Metastability and Strong Coupling.” Physical Review A,
vol. 107, no. 3, L031701, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L031701.
short: A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review
A 107 (2023).
date_created: 2023-04-09T22:01:00Z
date_published: 2023-03-22T00:00:00Z
date_updated: 2023-08-01T14:06:05Z
day: '22'
department:
- _id: JoFi
doi: 10.1103/PhysRevA.107.L031701
external_id:
arxiv:
- '2209.05165'
isi:
- '000957799000006'
intvolume: ' 107'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2209.05165
month: '03'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overcoming photon blockade in a circuit-QED single-atom maser with engineered
metastability and strong coupling
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2023'
...
---
_id: '12820'
abstract:
- lang: eng
text: "Disulfide bond formation is fundamentally important for protein structure,
and constitutes a key mechanism by which cells regulate the intracellular oxidation
state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen
peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally,
upon Cys oxidation PRDXs undergo extensive conformational rearrangements that
may underlie their presently structurally poorly defined functions as molecular
chaperones. Rearrangements include high molecular-weight oligomerization, the
dynamics of which are, however, poorly understood, as is the impact of disulfide
bond formation on these properties. Here we show that formation of disulfide bonds
along the catalytic cycle induces extensive microsecond time scale dynamics, as
monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly
and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics
to structural frustration, resulting from conflicts between the disulfide-constrained
reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis
data repository contains NMR data presented in the associated manuscript"
article_processing_charge: No
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Schanda P. Research data of the publication “Disulfide-bond-induced structural
frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820
apa: Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.”
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820
chicago: Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced
Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’”
Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820.
ieee: P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural
frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute
of Science and Technology Austria, 2023.
ista: Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced
structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’,
Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820.
mla: Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced
Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.”
Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820.
short: P. Schanda, (2023).
contributor:
- contributor_type: researcher
first_name: Laura
last_name: Troussicot
- contributor_type: researcher
first_name: Björn M.
last_name: Burmann
corr_author: '1'
date_created: 2023-04-10T05:55:56Z
date_published: 2023-04-18T00:00:00Z
date_updated: 2024-10-09T21:05:30Z
day: '18'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.15479/AT:ISTA:12820
file:
- access_level: open_access
checksum: 54a619605e44c871214fb0e07b05c6bf
content_type: application/zip
creator: pschanda
date_created: 2023-04-14T09:39:33Z
date_updated: 2023-04-14T09:39:33Z
file_id: '12823'
file_name: data_deposition.zip
file_size: 54184807
relation: main_file
success: 1
- access_level: open_access
checksum: 8dede9fc78399d13144eb05c62bf5750
content_type: application/octet-stream
creator: pschanda
date_created: 2023-04-14T09:39:58Z
date_updated: 2023-04-14T09:39:58Z
file_id: '12824'
file_name: README
file_size: 4978
relation: main_file
success: 1
file_date_updated: 2023-04-14T09:39:58Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13095'
relation: used_in_publication
status: public
status: public
title: Research data of the publication "Disulfide-bond-induced structural frustration
and dynamic disorder in a peroxiredoxin from MAS NMR"
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...